The interplay between neoantigens and immune cells in sarcomas treated with checkpoint inhibition.

Introduction: Sarcomas are comprised of diverse bone and connective tissue tumors with few effective therapeutic options for locally advanced unresectable and/or metastatic disease. Recent advances in immunotherapy, in particular immune checkpoint inhibition (ICI), have shown promising outcomes in several cancer indications. Unfortunately, ICI therapy has provided only modest clinical responses and seems moderately effective in a subset of the diverse subtypes.

Prevalence, clinical, and demographic characteristics of concomitant dengue fever and leptospirosis among acute dengue fever patients in The Western Province of Sri Lanka.

Dengue and leptospirosis are hyperendemic diseases in Sri Lanka. We aimed to determine the prevalence and clinical manifestations of concomitant infections of leptospirosis and acute dengue infection (ADI) in clinically suspected dengue patients. A descriptive cross-sectional study was carried out in five hospitals in the Western Province, from December 2018 to April 2019.

Personalized HLA typing leads to the discovery of novel HLA alleles and tumor-specific HLA variants.

Accurate and full-length typing of the HLA region is important in many clinical and research settings. With the advent of next generation sequencing (NGS), several HLA typing algorithms have been developed, including many that are applicable to whole exome sequencing (WES). However, most of these solutions operate by providing the closest-matched HLA allele among the known alleles in IPD-IMGT/HLA Database.

DSNet: Automatic dermoscopic skin lesion segmentation.

Background And Objective: Automatic segmentation of skin lesions is considered a crucial step in Computer-aided Diagnosis (CAD) systems for melanoma detection. Despite its significance, skin lesion segmentation remains an unsolved challenge due to their variability in color, texture, and shapes and indistinguishable boundaries.

Methods: Through this study, we present a new and automatic semantic segmentation network for robust skin lesion segmentation named Dermoscopic Skin Network (DSNet).

Detecting the occluding contours of the uterus to automatise augmented laparoscopy: score, loss, dataset, evaluation and user study.

Purpose: The registration of a preoperative 3D model, reconstructed, for example, from MRI, to intraoperative laparoscopy 2D images, is the main challenge to achieve augmented reality in laparoscopy. The current systems have a major limitation: they require that the surgeon manually marks the occluding contours during surgery. This requires the surgeon to fully comprehend the non-trivial concept of occluding contours and surgeon time, directly impacting acceptance and usability.

Whole exome sequencing of sporadic patients with Currarino Syndrome: A report of three trios.

Currarino Syndrome is a rare congenital malformation syndrome described as a triad of anorectal, sacral and presacral anomalies. Currarino Syndrome is reported to be both familial and sporadic. Familial CS is today known as an autosomal dominant disorder caused by mutations in the transcription factor MNX1.

A potential founder variant in in three Norwegian families with warts, molluscum contagiosum, and T-cell dysfunction.

Background: Four patients from three Norwegian families presented with a common skin phenotype of warts, molluscum contagiosum, and dermatitis since early childhood, and various other immunological features. Warts are a common manifestation of (HPV), but when they are overwhelming, disseminated and/or persistent, and presenting together with other immunological features, a primary immunodeficiency disease (PIDD) may be suspected.

Methods And Results: The four patients were exome sequenced as part of a larger study for detecting genetic causes of primary immunodeficiencies.

Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders.

Background: Primary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions.

cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data.

Background: With advances in next generation sequencing technology and analysis methods, single nucleotide variants (SNVs) and indels can be detected with high sensitivity and specificity in exome sequencing data. Recent studies have demonstrated the ability to detect disease-causing copy number variants (CNVs) in exome sequencing data. However, exonic CNV prediction programs have shown high false positive CNV counts, which is the major limiting factor for the applicability of these programs in clinical studies.

Identification of copy number variants from exome sequence data.

Background: With advances in next generation sequencing technologies and genomic capture techniques, exome sequencing has become a cost-effective approach for mutation detection in genetic diseases. However, computational prediction of copy number variants (CNVs) from exome sequence data is a challenging task. Whilst numerous programs are available, they have different sensitivities, and have low sensitivity to detect smaller CNVs (1-4 exons).

Distance saturation product predicts health-related quality of life among sarcoidosis patients.

Background: Sarcoidosis is a chronic disease with different phenotypic manifestations. Health-related quality of life is an important aspect in sarcoidosis, yet difficult to measure. The objective of this study was to identify clinical markers predictive of poor quality of life in sarcoidosis patients that can be followed over time and targeted for intervention.

Invasive pulmonary aspergillosis in patients with COPD: a report of five cases and systematic review of the literature.

Background: There are increasing reports describing invasive pulmonary aspergillosis (IPA) in patients with chronic obstructive pulmonary disease (COPD) without the classic risk factors for this severe infection. The available literature on this association is based on case reports or small case series. The aim of this review is to systematically review these cases and describe the clinical features, diagnostic studies and outcome.